Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for RPLP0

Basic gene info.	Gene symbol	RPLP0
	Gene name	ribosomal protein, large, P0
	Synonyms	L10E\|LP0\|P0\|PRLP0\|RPP0
	Cytomap	UCSC genome browser: 12q24.2
	Genomic location	chr12 :120634502-120639014
	Type of gene	protein-coding
	RefGenes	NM_001002.3, NM_053275.3,
	Ensembl id	ENSG00000089157
	Description	60S acidic ribosomal protein P060S ribosomal protein L10Eacidic ribosomal phosphoprotein P0
	Modification date	20141207
dbXrefs	MIM : 180510
	HGNC : HGNC
	Ensembl : ENSG00000089157
	HPRD : 01610
	Vega : OTTHUMG00000169317
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPLP0
	BioGPS: 6175
	Gene Expression Atlas: ENSG00000089157
	The Human Protein Atlas: ENSG00000089157
Pathway	NCI Pathway Interaction Database: RPLP0
	KEGG: RPLP0
	REACTOME: RPLP0
	ConsensusPathDB
	Pathway Commons: RPLP0
Metabolism	MetaCyc: RPLP0
	HUMANCyc: RPLP0
Regulation	Ensembl's Regulation: ENSG00000089157
	miRBase: chr12 :120,634,502-120,639,014
	TargetScan: NM_001002
	cisRED: ENSG00000089157
Context	iHOP: RPLP0
	cancer metabolism search in PubMed: RPLP0
	UCL Cancer Institute: RPLP0
Assigned class in ccmGDB	C

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Phenotypic Information for RPLP0(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: RPLP0
	Familial Cancer Database: RPLP0

* This gene is included in those cancer gene databases.

						.
Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: RPLP0
	MedGen: RPLP0 (Human Medical Genetics with Condition)
	ClinVar: RPLP0
Phenotype	MGI: RPLP0 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: RPLP0

Mutations for RPLP0

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPLP0 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG180012	PPP3CB	30	587	10	75230844	75239128	RPLP0	581	671	12	120634509	120634606
AF155662	RPLP0	41	210	12	120634611	120635169	NDUFA13	209	721	19	19627042	19639007
AI765188	RPLP0	27	206	12	120634505	120634684	MTMR10	201	470	15	31251088	31253198
BE698288	RPLP0	1	75	12	120636993	120637174	CDS1	65	90	4	85522777	85522802
AF132973	RPLP0	41	216	12	120634611	120635175	NDUFA13	217	718	19	19627052	19639006
BC000673	RTEL1	10	1349	20	62289713	62305447	RPLP0	1344	1722	12	120634505	120635270

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr12:120636469-120636469	p.I180S	2
chr12:120635197-120635197	p.S240S	2
chr12:120634697-120634697	p.A278G	2
chr12:120635133-120635133	p.A262T	1
chr12:120636422-120636422	p.G196S	1
chr12:120637115-120637115	p.E76E	1
chr12:120635143-120635143	p.T258T	1
chr12:120636466-120636466	p.S181F	1
chr12:120637168-120637168	p.T59A	1
chr12:120635152-120635152	p.T255T	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	3		3	1		5		1			4	2	1		1	1	4		5
# mutation	1	3		3	1		5		1			4	3	1		1	1	4		5
nonsynonymous SNV	1	1		2	1		2		1			3	3				1	3		5
synonymous SNV		2		1			3					1		1		1		1

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr12:120635197	p.T255T,RPLP0	2
chr12:120635152	p.S240S,RPLP0	2
chr12:120635168	p.Q191H,RPLP0	1
chr12:120636497	p.W9R,RPLP0	1
chr12:120637257	p.S181F,RPLP0	1
chr12:120635190	p.D308D,RPLP0	1
chr12:120636693	p.I180S,RPLP0	1
chr12:120637264	p.E302E,RPLP0	1
chr12:120636708	p.E171K,RPLP0	1
chr12:120638562	p.A262T,RPLP0	1

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for RPLP0 in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for RPLP0

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


EEF1G,RPL10,RPL10A,RPL11,RPL13A,RPL18A,RPL27A, RPL36,RPL37A,RPL4,RPL6,RPL7A,RPLP0,RPLP1, RPLP2,RPS10,RPS18,RPS2,RPS8,RPSA,RPSAP58	EEF1B2,EEF1G,EIF3D,GNB2L1,IMPDH2,NOB1,RPL10, RPL10A,RPL12,RPL14,RPL37,RPL4,RPL6,RPLP0, RPS18,RPS2,RPS5,RPS6,RPS7,RPS8,RPSAP58

LRRC75A-AS1,RPL10A,RPL12,RPL13A,RPL18,RPL35,RPL36, RPL41,RPL7A,RPLP0,RPLP1,RPS11,RPS14,RPS15, RPS16,RPS19,RPS29,RPS3,RPS5,RPS8,RPS9	AHCY,PHB2,RPL10,RPL13A,RPL18,RPL18A,RPL19, RPL29,RPL32,RPL7A,RPL8,RPLP0,RPLP1,RPS11, RPS14,RPS3,RPS5,RPS6,RPS8,RPSA,RPSAP58

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for RPLP0

There's no related Drug.

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Cross referenced IDs for RPLP0

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information